1FZA

CRYSTAL STRUCTURE OF FIBRINOGEN FRAGMENT D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin.

Spraggon, G.Everse, S.J.Doolittle, R.F.

(1997) Nature 389: 455-462

  • DOI: https://doi.org/10.1038/38947
  • Primary Citation of Related Structures:  
    1FZA, 1FZB

  • PubMed Abstract: 

    In blood coagulation, units of the protein fibrinogen pack together to form a fibrin clot, but a crystal structure for fibrinogen is needed to understand how this is achieved. The structure of a core fragment (fragment D) from human fibrinogen has now been determined to 2.9 A resolution. The 86K three-chained structure consists of a coiled-coil region and two homologous globular entitles oriented at approximately 130 degrees to each other. Additionally, the covalently bound dimer of fragment D, known as 'double-D', was isolated from human fibrin, crystallized in the presence of a Gly-Pro-Arg-Pro-amide peptide ligand, which simulates the donor polymerization site, and its structure solved by molecular replacement with the model of fragment D.


  • Organizational Affiliation

    Center for Molecular Genetics, University of California, San Diego, La Jolla 92093-0634, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN
A, D
87Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens)
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Go to UniProtKB:  P02671
PHAROS:  P02671
GTEx:  ENSG00000171560 
Entity Groups  
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UniProt GroupP02671
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN
B, E
328Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens)
Explore P02675 
Go to UniProtKB:  P02675
PHAROS:  P02675
GTEx:  ENSG00000171564 
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UniProt GroupP02675
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN
C, F
319Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
PHAROS:  P02679
GTEx:  ENSG00000171557 
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UniProt GroupP02679
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.363 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.72α = 90
b = 48.08β = 105.7
c = 167.56γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary